When I edit from the shell i have no problem and i never edit through FTP.

The problem is when i want to save changes through the administration interface (for example of joomla).

Through the admin interface of joomla you can change some parameters of the main configuration.php file on the fly (and with a easier way) without the need to edit the file from the shell. The same happens with templates parameters file (params.ini) that is also editable through the admin section of joomla.

Ok. Now please create a FTP user and use a external FTP clint like the FireFTP firefox plugin to connect to the site, donload CHANGELOG.php php to your workstation and edit a line in it and the upload iat again into the webspace. Does it work and if not, post the exact error messages from fireftp.